5K8C

X-ray structure of KdnB, 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, from Shewanella oneidensis

5K8C の概要

• エントリーDOI: 10.2210/pdb5k8c/pdb
• 分子名称: 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, PHOSPHATE ION, ... (7 entities in total)
• 機能のキーワード: group iii alcohol dehydrogenase, 8-amino-3, 8-dideoxy-d-manno-octulosonic acid, deoxy sugar, transferase
• 由来する生物種: Shewanella oneidensis (strain MR-1)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 40722.25

構造登録者

Holden, H.M.,Thoden, J.B.,Zachman-Brockmeyer, T.R. (登録日: 2016-05-28, 公開日: 2016-06-15, 最終更新日: 2023-09-27)

主引用文献

Zachman-Brockmeyer, T.R.,Thoden, J.B.,Holden, H.M.
Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-d-Manno-Octulosonic Acid.
Biochemistry, 55:4485-4494, 2016

PubMed Abstract: 8-Amino-3,8-dideoxy-d-manno-octulosonic acid (Kdo8N) is a unique amino sugar that has thus far only been observed on the lipopolysaccharides of marine bacteria belonging to the genus Shewanella. Although its biological function is still unclear, it is thought that the sugar is important for the integrity of the bacterial cell outer membrane. A three-gene cluster required for the biosynthesis of Kdo8N was first identified in Shewanella oneidensis. Here we describe the three-dimensional structures of two of the enzymes required for Kdo8N biosynthesis in S. oneidensis, namely, KdnB and KdnA. The structure of KdnB was solved to 1.85-Å resolution, and its overall three-dimensional architecture places it into the Group III alcohol dehydrogenase superfamily. A previous study suggested that KdnB did not require NAD(P) for activity. Strikingly, although the protein was crystallized in the absence of any cofactors, the electron density map clearly revealed the presence of a tightly bound NAD(H). In addition, a bound metal was observed, which was shown via X-ray fluorescence to be a zinc ion. Unlike other members of the Group III alcohol dehydrogenases, the dinucleotide cofactor in KdnB is tightly bound and cannot be removed without leading to protein precipitation. With respect to KdnA, it is a pyridoxal 5'-phosphate or (PLP)-dependent aminotransferase. For this analysis, the structure of KdnA, trapped in the presence of the external aldimine with PLP and glutamate, was determined to 2.15-Å resolution. The model of KdnA represents the first structure of a sugar aminotransferase that functions on an 8-oxo sugar. Taken together the results reported herein provide new molecular insight into the biosynthesis of Kdo8N.

PubMed: 27275764
DOI: 10.1021/acs.biochem.6b00439

実験手法

X-RAY DIFFRACTION (1.85 Å)